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Thread: Ancient I-M253 samples list

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    Quote Originally Posted by spruithean View Post
    Thanks for sharing that link, I'll give it a listen, any discussion mentioning I1, even if briefly, is probably important. I don't see very much discussion of I1 on most of the big blogs such as Eurogenes or Quiles Indo-European blog.



    Don't tell anyone at Eurogenes about this collaboration! I know there is some rivalry between the two camps in terms of what ancient people brought R1a or R1b and spoke this or that language

    I hope that Mr. Provyn is willing to go through with corrections of the aDNA samples that you've examined. It is certainly a bit strange that these papers used old forms of ISOGG when most of us have moved on and refer to haplogroups with the main root and terminal SNP method.




    I'm not familiar with URM035 and URM045, however if there were errors and broad haplogroup designations in the paper such as "BCDEF" that seems a bit suspect and warrants deeper investigation, interesting that it is designated I-Z60/Z61 in the spreadsheet. That could be very interesting if confirmed. I think most ancient I1 we'll find will be Migration Period and within the Medieval period (and of course the higher middle ages up to colonial eras). Obvious places to look are already being looked at as of late.

    I suspect that AE 1154 may be a error, I've not seen that sample anywhere in that paper and I've scoured it a few times. However perhaps it is referencing something else that may flown under the radar that was picked up recently. Perhaps time will tell.
    I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

    Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa...NCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

    I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

    I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

    Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.

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    I'm a little confused with the "hitched a ride" from the invaders, a ride to where exactly? Europe? Scandinavia? How does that make any sense if I1 is most likely native to Northern Europe? Hitched a ride to the steppe women? Disneyland? I don't understand what those words are supposed to convey, it needs to be clarified.
    What seems fairly evident so far is that I1 probably started to spread throughout Europe from Northern Europe only about 2000 years ago with ancient Germanic peoples and at that point BB and Corded Ware were already ancient history.

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    Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

    "The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

    Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

    It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."
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    Quote Originally Posted by spruithean View Post
    I had been hoping some comments about I1 would appear in that thread. A commenter under the name "Angantyr" claims that Nordic_LN II RISE179 is I1. That sample is on deadly's ancient I1 map as a pre-I1. Which I believe is appropriate as it is a low coverage sample and it was no call for ">99%" of the defining I1 SNPs.

    I think we can't be too lenient (but can't be too strict either) on what we define as I1. We already know I1 has a young TMRCA so true I1 will be in that timeframe.

    EDIT: keep your eye on this Eurogenes post, the comments are getting quite interesting!
    That's exactly why I've gone for pre-I1 rather than I1. RISE179 has derived calls for only two of the 312 SNPs that define the I1 haplogroup. Put it another way, I's say that I'd assign 2/312=0.64% confidence that RISE179 was an individual that had derived mutations for all of the I1 SNPs. Some of those no calls could be ancestral, or they could all be derived to make RISE179. I just think there's too much uncertainty to say I1 for sure. And both of the derived calls are one read SNPs which can be false positive. SVK-A1 from the ancient Iceland paper has a one-read derived call for Z131+, but that doesn't make SVK-A1 part of I-Z131 branch, especially when further digging shows a lot more cooroborating evidence that he's actually I-FGC21682.

    I feel that RISE179 shouldn't be ignored and is of interest (which is why that sample is on the map), but given the low quality and coverage in the BAM file I wouldn't consider is as exhibit A or a star piece of evidence to make any points regarding I1 haplogroup.

    You also make a good point about not being too lenient or too strict on what defines I1. Definitelty agree that we shouldn't ring fence ourselves too heavily on what we don't know, and revise criteria as definition as we go on. As an example, check out the ISOGG Y tree for haplogroup I in 2009 which is only 10 years ago - so much unknown compared to today: https://isogg.org/tree/2009/ISOGG_HapgrpI09.html

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    Quote Originally Posted by JonikW View Post
    I wonder whether deadly77 and other well versed experts on ancient I1 see any implications for us here. Very interesting.

    Edit: it kind of goes with what I posted earlier today on Scandinavia but I don't know what to make of any of it. I'm sure someone sees the bigger picture. I guess a small population of I1 got involved early on with the invaders, got lucky and expanded quite rapidly.

    http://eurogenes.blogspot.com/2019/0...e-age.html?m=1
    Cheers, but I'd say that what I bring to the table is understanding how to read the raw data and fit that into a Y-DNA phylogenetic tree. I'd say I'm much less well read on the populations, tribal groups and migrations of those time periods. I feel that a lot of you guys have a better handle on some of those aspects than I do. Most of my interest in history before getting interested in DNA is from later time periods, but have found a lot of this rather fascinating and learning a lot as I go along and keen to learn more.

    I haven't got too involved in the population genetics discussions using primarily autosomal DNA as my learning curve and familiarity with autosomal DNA hasn't got to the same point as where I am with Y-DNA. I read some of the discussions and I think I understand the outputs and graphs, although I'm not as clear on how the data is put together and how things work "under the hood" in the same way that I approach Y-DNA. More to learn, but I feel that there's a lot of hand-waving and bias in some of those discussions - and I mean generally rather than specifically referring to the linked post - and that is also the case for some of the Y-DNA discussions as well. Probably my background as a scientist (although not in genetics or biology) that makes me a bit wary of taking too much at face value.

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    Quote Originally Posted by JonikW View Post
    Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

    "The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

    Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

    It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."
    Yeah, I'd agree with that. Not impossible, but I agree it would be unlikely - but sometimes you can find needles in haystacks. But not always.

    Also agree with the founder effect point. This paper by Batini et al in Nature Communications 2015 compares this (article is open access) https://www.nature.com/articles/ncomms8152 using SNP data and we can see it in the STR convergence of our match lists - or as Robin Spencer more appropriately calls it a lack of STR divergence from a recent founder on his Tracking Back Website: http://scaledinnovation.com/gg/gg.html?rr=convergence

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    Quote Originally Posted by deadly77 View Post
    I've found the Insitome podcast really interesting as a series - they also cover a lot of different areas in other blog posts. Really worth listening to.

    Yes, Hunter says thanks and he will update the spreadsheet with corrections. I've discussed a few things with him before and I think he's keen to have accuracy. He's put a short video on YouTube discussing the collaboration on these ancient samples with Carlos Quiles and Vadim Urasin from YFull here https://www.youtube.com/watch?v=zjQa...NCMshz5F5PNTeU his main goal appears to be getting the data into a format that's compatible with his Phylogeographer tool.

    I think the longhand nomenclature for persists due to familiarity of those who have likely used that nomenclature for years. As a relative latecomer, I often have to look those up and translate the alphabet soup. I much prefer I-L338 rather than I1a2a1a1a1a1 (as defined by 2019 ISOGG tree). The longhand nomenclature also changes from year to year on the ISOGG tree, which is where I think Carlos Quiles is making mistakes in I1 subclades in his spreadsheet regarding the ancient Iceland genomes. The supplementary information in that Science 2018 paper defines that the authors are using the 2016 version of the ISOGG tree - as long as you follow that, there's no conflict - SSJ-A2 is I1a1b3 which is I-Z74, HSJ-A1 is I1a1b3b which is I-L813, SBT-A1 is I1a2a1a2 which is I-F2642. All fine. Problem comes when Carlos Quiles takes the longhand data of these samples and then looks at a later version of the ISOGG tree and incorrectly interprets SSJ-A2 and HSJ-A1 as I-A8182 and SBT-A1 as I-S26062. It's another arguement for moving on from this obsolete nomenclature to avoid the confusion.

    I haven't done full analysis of urm035 and urm 045 yet, but the assignments are matching up with the BAM files - urm035 has derived calls for DF29 and Z2892/CTS9848 but an ancestral call for Z2893 among the I-DF29 branch. Also one read ancestral for Z59 and Z140 so far. urm045 has derived calls for Z2893 and Z2892/CTS9848 among the I-DF29 branch and derived for S439/Z61. All these are one read SNPs so not solid yet and I'll dig a bit deeper and see if there's a bit more evidence. Probably not reported in paper as any indentifying Y-SNPs were below threshold for reporting or they weren't looking in the right places. They did get 84005 as I1a1b3/I-Z74 in the paper though.

    Yeah, I havent found AE 1154 either - in the paper or at ENA (where the other three I1 from that paper are). It could be a mis-transcription of AED249 that we already know about.
    That's pretty frustrating that Mr. Quiles would do it that way but I suppose he's not alone, and it's pretty disappointing that the teams working on these ancient DNA works would be so neglectful of the fact that the ISOGG nomenclature and alphabet soup change every year, the only thing that doesn't change is the shorthand nomenclature. I-L338 is always I-L338, this way confusion is very low. I can't even look at older mentions (or newer mentions) of R1b and R1a clades if they don't have their terminal SNP mentioned. The size of some of those alphabet soups for R1 clades is ridiculous

    Keep us posted on those urm guys, they could get really interesting and even a tentative placement as simply I-DF29 for both is a hell of lot better than "ND" and "BCDEF". I was reading (yet again) the Sigtuna paper yesterday, quite an interesting read in terms of where some of these people likely came from in relation to Sigtuna.

    Thanks again for all the work you do on these BAM files, it's definitely not something I'm able to do, or probably capable of

    So Hunter refers to YFulls data? I had wondered as there is another phylogeography tracker that seems based off of FTDNA's data, which the creator of that site has begun posting here. http://scaledinnovation.com/gg/snpTracker.html , For my SNP, Hunter's tracker and the above tracker are a fair bit different in terms of dating and I suppose naming. YFull still has A14097 lumped in with A14094 (my fault really as I've been tardy with anything related to sending off data to them), while the other has A14097 above A14094/M4050. Not too big of a deal though.

    I had suspected that AE sample to be a typo. Seemed to similar in the beginning to AED.

    Quote Originally Posted by oz View Post
    I'm a little confused with the "hitched a ride" from the invaders, a ride to where exactly? Europe? Scandinavia? How does that make any sense if I1 is most likely native to Northern Europe? Hitched a ride to the steppe women? Disneyland? I don't understand what those words are supposed to convey, it needs to be clarified.
    What seems fairly evident so far is that I1 probably started to spread throughout Europe from Northern Europe only about 2000 years ago with ancient Germanic peoples and at that point BB and Corded Ware were already ancient history.
    I think Razib Khan was simply saying that I1 carriers hitched a ride with these R1b rich groups wherever it may have been and "prospered" off the fortune of these R1b clans. This could have happened anywhere, and given the proliferation of I1 probably occured in the Bronze Age it could have happened in Northern Europe? I didn't quite get the impression that he was implying (totally) I1 literally hitched a migratory ride somewhere with the R1b folks, more that it was just benefit by association. Perhaps a bit parasitic...

    I wish we had more definitive answers, I1 is a missing link in a lot of the ancient DNA...

    Quote Originally Posted by JonikW View Post
    Thanks again for your wonderful work deadly77. I see now this comment from David in his Nordic thread:

    "The high frequencies of U106 and I1 in Scandinavia are best explained by extreme local founder effects during the Bronze Age.

    Not migrations of U106 and I1 rich populations into Scandinavia from, say, the Carpathian Basin.

    It's unlikely that anyone will find the relevant, ancestral I1 in the ancient DNA before the founder effect. That is, dating to the TRB, Battle Axe or BB periods."
    Exactly this, which sort of fits with the definition, (stay with me here my brain is not cooperating today), I1's TMRCA is sometime in the Bronze Age if the YFull and other TMRCA estimates are correct, that places it sometime in 27th-25th century BC if not earlier or later (some context, the Instructions of Shuruppak were likely written sometime in the space of 2600 to 2500 BCE). So I1 came out of hiding at some point around this time, yet we've found potential I1 samples pre-dating this by a long time as BAB5 is dated to around 5600-4900 BCE, and BAL051 is dated even earlier than that. However their SNP calls are rather underwhelming for being definitive for being I1-M253. This is why deadly and several others have begun to label these samples as pre-I1 (including the Nordic LN and BA guys), but we already know that I1's split from I2 is likely quite some time before I1 really started expanding, so it's not necessarily a surprise that we find pre-I1 or quasi-I1 lineages in strange places.

    Quote Originally Posted by deadly77 View Post
    That's exactly why I've gone for pre-I1 rather than I1. RISE179 has derived calls for only two of the 312 SNPs that define the I1 haplogroup. Put it another way, I's say that I'd assign 2/312=0.64% confidence that RISE179 was an individual that had derived mutations for all of the I1 SNPs. Some of those no calls could be ancestral, or they could all be derived to make RISE179. I just think there's too much uncertainty to say I1 for sure. And both of the derived calls are one read SNPs which can be false positive. SVK-A1 from the ancient Iceland paper has a one-read derived call for Z131+, but that doesn't make SVK-A1 part of I-Z131 branch, especially when further digging shows a lot more cooroborating evidence that he's actually I-FGC21682.

    I feel that RISE179 shouldn't be ignored and is of interest (which is why that sample is on the map), but given the low quality and coverage in the BAM file I wouldn't consider is as exhibit A or a star piece of evidence to make any points regarding I1 haplogroup.

    You also make a good point about not being too lenient or too strict on what defines I1. Definitelty agree that we shouldn't ring fence ourselves too heavily on what we don't know, and revise criteria as definition as we go on. As an example, check out the ISOGG Y tree for haplogroup I in 2009 which is only 10 years ago - so much unknown compared to today: https://isogg.org/tree/2009/ISOGG_HapgrpI09.html
    I definitely agree that we should stick with caution with how these old samples are labeled indeed. I'm definitely not saying we should ignore the pre-I1 samples, those are likely important, even if they might be extinct lineages, they at least give us a picture of how dispersed I1 related lineages could have been. We know YFull still estimates the formation of I1 to be 27,500 years ago in regards to when it split from I2.

    Ah, the old ISOGG 2009 tree, I think that was when FTDNA had finally determined that my bunch weren't just I-M170 and that we were in the I-M253 haplogroup.

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    Quote Originally Posted by deadly77 View Post
    Cheers, but I'd say that what I bring to the table is understanding how to read the raw data and fit that into a Y-DNA phylogenetic tree. I'd say I'm much less well read on the populations, tribal groups and migrations of those time periods. I feel that a lot of you guys have a better handle on some of those aspects than I do. Most of my interest in history before getting interested in DNA is from later time periods, but have found a lot of this rather fascinating and learning a lot as I go along and keen to learn more.

    I haven't got too involved in the population genetics discussions using primarily autosomal DNA as my learning curve and familiarity with autosomal DNA hasn't got to the same point as where I am with Y-DNA. I read some of the discussions and I think I understand the outputs and graphs, although I'm not as clear on how the data is put together and how things work "under the hood" in the same way that I approach Y-DNA. More to learn, but I feel that there's a lot of hand-waving and bias in some of those discussions - and I mean generally rather than specifically referring to the linked post - and that is also the case for some of the Y-DNA discussions as well. Probably my background as a scientist (although not in genetics or biology) that makes me a bit wary of taking too much at face value.
    I'd say the Bronze Age or so is a bit early to be thinking of specific Germanic tribes, as they are relatively late compared to the Gallic tribes, Thracians, Illyrians, and Scytho-Sarmatian groups we hear about earlier in records.

    I'm with you on the autosomal DNA, while it is fascinating and it can be entertaining to see where one plots in the grand scheme of things or where "fit" in relation to various ancient populations it can seem like some people have a bit of bias towards what they want their generated results to "say". I'm also not sure I'm skilled enough to design ways to calculate my own potential best fits with these new calculators like G25 or nMonte.

    Though I do find the autosomal calculations quite interesting in relation to ancient populations like Goths, Gepids, Scythians, Celts, Bronze Age peoples, etc.

    Quote Originally Posted by deadly77 View Post
    Yeah, I'd agree with that. Not impossible, but I agree it would be unlikely - but sometimes you can find needles in haystacks. But not always.

    Also agree with the founder effect point. This paper by Batini et al in Nature Communications 2015 compares this (article is open access) https://www.nature.com/articles/ncomms8152 using SNP data and we can see it in the STR convergence of our match lists - or as Robin Spencer more appropriately calls it a lack of STR divergence from a recent founder on his Tracking Back Website: http://scaledinnovation.com/gg/gg.html?rr=convergence
    Thanks for linking that study, I had seen some of the images of it, but I guess it slipped my mind to actually go looking for it , I've seen my own cases of convergence in my end of the F2642 tree. A few years ago I had a match to some Danish families with a similar surname to my own and in all honesty the surnames were essentially identical, just in different languages and I initially wondered if it was a legitimate match, however Big Y has shown that they are on a totally separate branch of F2642 (and they are more closely related to SBT-A1 than me). This is also seen closer to my part of the F2642 tree, especially between JMcB and myself. My family's haplotype is a reasonable match to several of JMcB's group however Big Y again showed that we are basically on sibling branches of the F2642 tree. I think if it wasn't for NGS I'd probably still be pursuing false leads.

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    Just to share some Polish ancient I1...

    This was originally posted by Tomenable on another forum

    All of these samples are from 7 locations:

    Late Iron Age (dates) samples:

    KO = Kowalewko (100-300 AD)
    MZ = Maslomecz (200-400 AD)

    Early Medieval (dates) samples:

    NA = Niemcza (900-1000 AD)
    SI = Sowinki (1000-1100 AD)
    LO = Legowo (1000-1200 AD)
    GO = Gniezno (1000-1200 AD)
    ME = Markowice (1000-1200 AD)



    I'm not sure which samples are I1, but two, KO_55 and ME_7 are certainly I1:

    KO_55, Kowalewko (100-300 AD), I1a3a1a1-Y6626
    KO_45, Kowalewko (100-300 AD), I2a2a1b2a-L801
    KO_22, Kowalewko (100-300 AD), G2a2b-L30
    KO_57, Kowalewko (100-300 AD), G2a2b-L30

    ME_7, Markowice (1000-1200 AD), I1a2a2a5-Y5384
    NA_13, Niemcza, (900-1000 AD), I2a1b2-L621
    NA_18, Niemcza, (900-1000 AD), J2a1a-L26

    Other confirmed males (but no Y-DNA assignment) include:

    Ancient group (3): KO_18, KO_36, KO_8
    Medieval (7): NA_29, NA_2, NA_3, ME_4, LO_5, SI_10, SI_11

    In total there must be 9 samples of I1, because ME_7 is not included here:

    https://www.academia.edu/33791135/20..._DNA_libraries

    Only samples from Kowalewko, Maslomecz, Legowo and Niemcza are here.

    So I1a2a2a5-Y5384 from Early Medieval Markowice is our 9th sample of I1
    Credit goes to Tomenable.

    Perhaps some of these could go to the ancient I1 map at some point, perhaps if they are fully vetted, or tentatively added for now? I should add that the Kowalewko samples have been attributed to the Wielbark culture (AFAIK) which is where the early Goths, Gepids and Rugii were believed to have originated before migrating onward to the Chernyakhov cultural sphere.
    Last edited by spruithean; 05-23-2019 at 06:05 PM.

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    Quote Originally Posted by spruithean View Post
    Just to share some Polish ancient I1...

    This was originally posted by Tomenable on another forum



    Credit goes to Tomenable.

    Perhaps some of these could go to the ancient I1 map at some point, perhaps if they are fully vetted, or tentatively added for now? I should add that the Kowalewko samples have been attributed to the Wielbark culture (AFAIK) which is where the early Goths, Gepids and Rugii were believed to have originated before migrating onward to the Chernyakhov cultural sphere.
    So the Wielbark one is L338 unless I'm missing something. I hope we can reach a little further downstream on that. Interesting.
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    mtDNA: traces to Glamorgan, Wales, 18th century. Mother's Y line (Wales): R-L21 L371

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